Use the reasoner of the library owlready2 on an ontology already in a file

I have used owlready2 (https://owlready2.readthedocs.io/en/latest/)

I'm trying to

1. read an ontology on disk (onto.xml)
2. add a swrl rule
3. run the reasoner on it
4. and then save the resulting ontology with the new facts inferred.

I'm a bit stuck right now.

I tried the examples, but I cannot understand why I have to define classes in the python program (https://owlready2.readthedocs.io/en/latest/rule.html) I tried this but I already have Classes, ObjectProperties and the Individuals in my onto.xml.

Defining classes, objectproperties and individuals all in the python works, the reasoner answers.

My prefered examples are this kind https://stackoverflow.com/questions/69224096/swrl-rules-in-owl-2/78320189 with the brothers and uncles, quite easy to follow.

Bye

Here's a basic_reader.py

#!/usr/bin/env python3
# Owlready2 currently reads the following file format: RDF/XML, OWL/XML, NTriples. The file format is automatically detected.
import argparse
import os

import owlready2 as owl

parser = argparse.ArgumentParser()
parser.add_argument("--ontology", help="ontology file", required=True)
args = parser.parse_args()

path2in = args.ontology
onto = owl.get_ontology(path2in).load()

print(list(onto.classes()))

print(list(onto.individuals()))

That works with an ontology on a file

if you ontology is in ttl format you can convert it on the fly like this :

#!/usr/bin/env python3
# Owlready2 currently reads the following file format: RDF/XML, OWL/XML, NTriples. The file format is automatically detected.
import argparse
import os

import owlready2 as owl

parser = argparse.ArgumentParser()
parser.add_argument("--ontology", help="ontology file as a ttl file", required=True)
args = parser.parse_args()

path2in = args.ontology
path2out = path2in.replace(".ttl", ".xml")

cmd2 = f"ontospy ser -f xml {path2in} 2>/dev/null > {path2out}"
os.system(cmd2)


onto = owl.get_ontology(path2out).load()

print(list(onto.classes()))

print(list(onto.individuals()))

I reply to myself with this working example :

def main():
    """add a swrl rule."""
    parser = argparse.ArgumentParser()
    parser.add_argument("--ontology", help="ontology file", required=True)
    parser.add_argument(
        "--destination", help="destination ontology file", required=True
    )

    args = parser.parse_args()

    input_file = args.ontology
    output_file = args.destination

    onto = owl.get_ontology(input_file).load()

    with onto:
        swrl_rule = """ http://maccve/onto#Machine(?m) ^ http://maccve/onto#Package(?p) ^ http://maccve/onto#CVE(?c) ^ http://maccve/onto#mcontains(?m, ?p) ^ http://maccve/onto#has_CVE(?p, ?c) -> http://maccve/onto#contains_CVE(?m, ?c) """

        rule = owl.Imp()
        rule.set_as_rule(swrl_rule)
        onto.save(file=output_file, format="rdfxml")

if __name__ == "__main__":
    main()

So let's try with this ontology

@prefix : <http://maccve/onto#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .

:Machine a owl:Class .
:CVE a owl:Class .
:Package a owl:Class .

# Machine contains Package
:mcontains a owl:ObjectProperty ;
         rdfs:domain :Machine ;
         rdfs:range :Package .

# Package has_CVE CVE
:has_CVE a owl:ObjectProperty ;
         rdfs:domain :Package ;
         rdfs:range :CVE .

# Cette property est determinée par swrl
:contains_CVE a owl:ObjectProperty ;
         rdfs:domain :Machine ;
         rdfs:range :CVE .


:www1 a owl:NamedIndividual, :Machine .
:www2 a owl:NamedIndividual, :Machine .

:apache12 a owl:NamedIndividual, :Package .
:apache22 a owl:NamedIndividual, :Package .

:CVE1212 a owl:NamedIndividual, :CVE .

:www1 :mcontains :apache12 .
:www2 :mcontains :apache22 .
:apache22 :has_CVE :CVE1212 .

if the rule work it will infer that machine :www2 :mcontains a :CVE1212

The tool must take an xml in input, so before adding the rule you must convert it to xml